Transcription
Explain the Central Dogma of Genetics
Genomic DNA undergoes transcription which results in an mRNA molecules that mRNA molecule undergoes translation, that results in the formation of a POLYPEPTIDE.
DNA -> mRNA -> Polypeptide
The release of the sigma factor marks the transition to the elongation stage of transcription.
More than one codon can code for the SAME amino acid.
The genetic code is widely universal
and is used by viruses, prokaryotes, fungi, plants and animals.
Where in the ribosomal subunit of bacterial translation do the following occur:
A) mRNA - tRNA recognition
B)peptidyl transfer reaction
C) Exit of the polypeptide from the ribosome.
D) Binding of Initiation Factors IF1,IF2 and IF3.
a) on the surface of the 30 s subunit/interface between the two subunits.
b)within the 50s subunit
c)within the 50s subunit
d) within the 30s subunit.
If you're lactose intolerant what structural genes do you have trouble making?
Lac Z Lac Y and Lac A.
A mutation within the DNA sequence of a certain gene changes the start codon to a stop codon. How will this mutation affect the transcription of this gene?
The mutation will not affect transcription. But it will affect translation by preventing the initiation of polypeptide synthesis.
How does the sigma factor recognize the bacterial promoter? what type of bonding occurs?
Sigma factor slides along the major groove. Its ale to recognize the base sequences exposed in the groove. It undergoes hydrogen bonding when it recognizes the promoter sequence.
if we assume that the tRNAs do not contain modified bases, what is the minimum number of tRNAs needed to recognize codons for each of the following amino acids?
Leucine:
Methionine:
Serine:
Leu: 3
there are 6 leucine codons
the anticodon AAU would recognize UUA and UUG. two other tRNA's are need to recognize the four other codons.
Met:1
there is only one MET codon AUG so the anticodon needed would be UAC.
Ser: 3
6 serine codons, only one is needed to recognize AGU and AGC. Two tRNAs are need to recognize the other four!
What sequence in bacterial mRNA promotes the recognition by the 30s subunit?
the Shine-Dalgarno sequence. It's needed for binding of the mRNA to the small ribosomal subunit.
sequence: UUAGGAGGU
If lactose is present it will bind to the ______ and keep it from binding to the operator _____ will bind to the _____.
Repressor, RNA polymerase, promoter.
An RNA transcript has the following sequence 5'-GGCAUGCAUUACGGCAUCACACUAGGGAUC-3' what does template strand look like?
3'-CCGTACGTAATGCCGTAGTGTHATCCTAH-5'
A) what types of mutations woud prevent rho independent termination
B) what type mutations would prevent rho dependent termination
C) if a mutation prevented transcriptional termination at the end of a gene where would gene transcription end?
a)Mutations that alter uracil rich region by introducing guanins and cytosines and mutations that prevent the formation of the stem loop structure.
b)mutations that alter termination sequences, and mutations that alter rho protein recognition site.
c)somewhere waaaay down stream, another termination sequence would be found, thats were termination would eventually occur.
If a tRNA molecule carries glutamic acid, what are the possible anticodon sequences that it could contain. Be specfic about hte 5' and 3' ends.
3'-CUU-5'
or
3'-CUC-5'
How does a eukaryotic ribosome select its start codon? Describe the sequences in eukaryotic mRNAs that optimize start codon recognition.
Ribosome binds at the 5' end of the mRNA and then scans in the 3' direction for the start codon (AUG). If it finds one that satifies Kozaks rules it will begin translation at that site.
-guanosine cap at the +4 position and a purine at the -3 position
If we wanted to make sure transcription did not happen, where would the repressor need to bind to ensure transcription couldn't happen.
The Operator.
Describe the processing events that occur during the production of tRNA in E.coli
the 5' end of the tRNA is cleaved by RNAseP
the 3' end is cleaved by a different endonuclease.
then a few nucleotides are degraded by an exonuclease that removes nucleotides until it reaches a CCA sequence.
cytosine - cytosine- adenine tail
What is a unique feature of ribozymes?
- its an RNA molecule with catalytic activity
it can act as a "self splicing" molecule --> splice without the help of a protein.
Describe the basic structures of tRNA molecules
-clover structure with 3 stem loops
- 2nd stem look has the anticodon sequence that recognizes the codon seq. in mRNA.
-3' end of each tRNA is an acceptor stem with the CCA sequence (attachment site for the amino acid.)
Explain the functional roles of the A, P, E site during translation.
A (aminoacyl site): tRNA carries a single amino acid and initially binds.
- 1 exception the INIATIOR tRNA molecule binds to the P site.
the growing chain is removed from the tRNA in the P site then transferred to the Amino acid attached to the tRNA in the A-site.
The ribosome moves in the 3' direction with two tRNA's in the P and A sites moved the E site and P site. The uncharged tRNA in the E site is then released.
If there is no lactose present, what happens?
We keep the genes turned off, the repressor is expressed. It binds to the operator to keep everything shut down.
Recall the functions of E.Coli RNA polymerase:
Haloenzymes: Alpha (2) Beta, Beta' , Sigma
What are the functions of the four subunits?
Alpha: assembly tetrameric core (gets everyone together)
Beta: ribonucleic triphosphate binding( make sure the enzymes bind).
Beta': DNA template binding region
Sigma: initiates transcription
Where does transcription initiation occur in
EUKARYOTES:
PROKARYOTES:
eukaryotes:
The initation site is located +1 of where transcription begins.
upstream sequences (bases before the iniation site)
downstream sequences (bases after the iniation site)
Prokaryotes:
The prokaryotic promoter is present upstream +1 site. -10 sequences, and -35 sequences.
Describe the components of eukaryotic ribosomal subunits and the location of where the assembly occurs within the living cells.
-33 proteins and one rRNA assemble the 40 s subunit.
-49 proteins and 3 rRNAs assemble the 60 s subunit.
assembly occurs in the nucleolus.
In which site ( A , P , E, sites) can the following be found?
A) tRNA without an amino acid attached
B) tRNA with a polypeptide attached
C) tRNA with a single amino attached
A) the E site and the P site (a tRNA without an amino acid attached is only briefly found in the P site b4 translation).
B) P site and A site (tRNA with polypeptide chain is only briefly found in the A site b4 translation).
C) Usually the A site ; except for the initiation tRNA which can be found in the P site.
If glucose is present do we need to express these genes to help metabolize lactose?
No, so the repressor is bound to the operator.
When glucose is present cyclic AMP concentration goes down. It binds to a protein called CAP, the function of CAP is help RNA polymerase stay on.
So if we have lactose but NO GLUCOSE --> it will bind to the repressor and keep the repressor from binding to the operator. But RNA polymerase and bind to the promotor.
Cyclic AMP will bind to cap both (RNA&CAP) binds, the polymerase takes off and express all the 3 lactose genes.
IF glucose and lactose are present, what does the cell prefer? Glucose
Lactose will bind to the repressor, because glucose is present cyclic amp is down, so CAP wont bind efficient, RNA polymerase will bind but not efficiently. Creates a basil level of these genes, may metabolize some lactose but not alll.